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- PDB-5e2g: Crystal Structure of D-alanine Carboxypeptidase AmpC from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 5e2g
TitleCrystal Structure of D-alanine Carboxypeptidase AmpC from Burkholderia cenocepacia
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / THIOCYANATE ION / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.651 Å
AuthorsKim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal Structure of D-alanine Carboxypeptidase AmpC from Burkholderia cenocepacia
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,78910
Polymers79,3212
Non-polymers4698
Water12,647702
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8955
Polymers39,6601
Non-polymers2344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8955
Polymers39,6601
Non-polymers2344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.965, 85.965, 90.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Beta-lactamase


Mass: 39660.250 Da / Num. of mol.: 2 / Fragment: residues 31-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: ampC, BCAS0156 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EPS2, beta-lactamase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.5 M potassium thioccyanate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 87979 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.093 / Net I/σ(I): 20.97
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.24 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.651→34.42 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 4479 5.1 %random
Rwork0.1501 ---
obs0.1528 87896 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 26 702 6022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065486
X-RAY DIFFRACTIONf_angle_d0.8857466
X-RAY DIFFRACTIONf_dihedral_angle_d13.7143260
X-RAY DIFFRACTIONf_chiral_restr0.05829
X-RAY DIFFRACTIONf_plane_restr0.005966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6507-1.67910.27162000.26893347X-RAY DIFFRACTION75
1.6791-1.70960.28891910.24463737X-RAY DIFFRACTION82
1.7096-1.74250.27492120.23283868X-RAY DIFFRACTION88
1.7425-1.77810.26552020.2224320X-RAY DIFFRACTION96
1.7781-1.81670.19762010.19724274X-RAY DIFFRACTION95
1.8167-1.85890.27332020.19584268X-RAY DIFFRACTION95
1.8589-1.90540.21452700.18964207X-RAY DIFFRACTION94
1.9054-1.95690.19941760.18574380X-RAY DIFFRACTION96
1.9569-2.01440.20372300.18254205X-RAY DIFFRACTION95
2.0144-2.07940.20542000.17034280X-RAY DIFFRACTION96
2.0794-2.15370.20162100.17544345X-RAY DIFFRACTION95
2.1537-2.23980.20472640.17734151X-RAY DIFFRACTION94
2.2398-2.34160.20742700.17074240X-RAY DIFFRACTION94
2.3416-2.46490.25092120.17414278X-RAY DIFFRACTION95
2.4649-2.61910.20732780.16214214X-RAY DIFFRACTION94
2.6191-2.82090.19912080.15454280X-RAY DIFFRACTION95
2.8209-3.1040.19252130.14254297X-RAY DIFFRACTION95
3.104-3.55140.16392120.12364283X-RAY DIFFRACTION95
3.5514-4.46780.14642350.10034236X-RAY DIFFRACTION95
4.4678-21.49310.13982090.11744262X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4233-0.07310.08261.39350.16030.783-0.0260.02690.20180.0474-0.12930.1675-0.2415-0.08570.09140.2277-0.0058-0.05660.1456-0.04140.1606-16.55619.64020.6408
21.20860.45580.54820.5041-0.08450.5040.1454-0.3651-0.12830.2393-0.1028-0.09090.1418-0.25220.02530.2624-0.0729-0.03420.22710.02960.1788-10.4101-1.75139.4029
31.8877-0.63920.21020.77070.23460.5185-0.1827-0.26620.08270.31620.01890.0323-0.2442-0.03360.13310.29060.0026-0.03860.1727-0.02550.1819-10.759919.352210.7888
40.90860.03510.27041.29290.3290.7395-0.08770.06550.08-0.0365-0.05220.108-0.1241-0.05010.1020.1695-0.011-0.03220.1564-0.01140.1358-16.944512.2955-6.9089
52.03220.8961-0.5741.70130.69830.8549-0.0721-0.2538-0.34730.2217-0.3170.51390.3863-0.52390.03670.309-0.09610.16130.2689-0.10120.4362-28.270621.681645.0478
61.5450.5548-0.41412.06660.04450.5637-0.05320.0992-0.1062-0.0968-0.046-0.03590.1442-0.04680.10610.21160.02030.05240.1374-0.02090.1408-10.701135.792335.1271
70.8737-0.7334-0.52731.22960.23750.42150.05660.14230.038-0.1573-0.04590.0034-0.0566-0.1155-0.00720.20750.04160.01430.18430.01440.1507-7.788645.934130.4197
82.45820.56910.48870.3570.49540.7465-0.14820.345-0.1234-0.2074-0.01650.24430.0978-0.18970.10680.33320.00290.03570.2598-0.07390.2401-16.758328.870826.4388
90.8373-0.0206-0.34491.20990.2760.7718-0.0771-0.055-0.09880.052-0.03670.12610.1458-0.04220.10760.17290.01510.04130.1433-0.01480.1513-17.04137.326746.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 355 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 29 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 100 )
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 177 )
8X-RAY DIFFRACTION8chain 'B' and (resid 178 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 355 )

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